Starting phenix.real_space_refine on Sat Jul 4 05:34:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7afk_11768/07_2026/7afk_11768_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7afk_11768/07_2026/7afk_11768.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7afk_11768/07_2026/7afk_11768_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7afk_11768/07_2026/7afk_11768_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7afk_11768/07_2026/7afk_11768.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7afk_11768/07_2026/7afk_11768.map" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 456 5.49 5 Mg 12 5.21 5 S 28 5.16 5 C 9845 2.51 5 N 3449 2.21 5 O 4730 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18521 Number of models: 1 Model: "" Number of chains: 11 Chain: "1" Number of atoms: 9758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 9758 Classifications: {'RNA': 456} Modifications used: {'rna2p_pur': 36, 'rna2p_pyr': 35, 'rna3p': 3, 'rna3p_pur': 212, 'rna3p_pyr': 170} Link IDs: {'rna2p': 71, 'rna3p': 384} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1753 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain: "C" Number of atoms: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1653 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 7, 'TRANS': 203} Chain: "G" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1181 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "I" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "J" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 795 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "M" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 883 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "N" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "S" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 658 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "1" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Unusual residues: {' MG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.06, per 1000 atoms: 0.22 Number of scatterers: 18521 At special positions: 0 Unit cell: (118.265, 116.095, 159.495, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 28 16.00 P 456 15.00 Mg 12 11.99 O 4730 8.00 N 3449 7.00 C 9845 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.41 Conformation dependent library (CDL) restraints added in 496.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 18 " 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2052 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 9 sheets defined 48.5% alpha, 14.3% beta 116 base pairs and 211 stacking pairs defined. Time for finding SS restraints: 2.92 Creating SS restraints... Processing helix chain 'B' and resid 5 through 13 removed outlier: 3.707A pdb=" N ALA B 12 " --> pdb=" O ASP B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Proline residue: B 29 - end of helix Processing helix chain 'B' and resid 42 through 63 Proline residue: B 48 - end of helix Processing helix chain 'B' and resid 76 through 86 Processing helix chain 'B' and resid 103 through 124 Processing helix chain 'B' and resid 130 through 149 Processing helix chain 'B' and resid 169 through 180 Processing helix chain 'B' and resid 192 through 196 removed outlier: 4.225A pdb=" N GLY B 195 " --> pdb=" O ASP B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 227 Processing helix chain 'C' and resid 6 through 11 Processing helix chain 'C' and resid 29 through 47 Processing helix chain 'C' and resid 72 through 78 Processing helix chain 'C' and resid 81 through 96 Processing helix chain 'C' and resid 108 through 112 Processing helix chain 'C' and resid 113 through 126 removed outlier: 3.619A pdb=" N ALA C 117 " --> pdb=" O ALA C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 145 Processing helix chain 'G' and resid 21 through 31 Processing helix chain 'G' and resid 35 through 54 removed outlier: 3.573A pdb=" N ALA G 46 " --> pdb=" O ILE G 42 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR G 49 " --> pdb=" O SER G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 70 removed outlier: 4.284A pdb=" N GLU G 63 " --> pdb=" O LEU G 59 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASN G 68 " --> pdb=" O VAL G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 112 removed outlier: 3.663A pdb=" N ARG G 96 " --> pdb=" O ARG G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 129 removed outlier: 3.516A pdb=" N SER G 125 " --> pdb=" O ALA G 121 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP G 126 " --> pdb=" O ASN G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 148 removed outlier: 3.613A pdb=" N ALA G 145 " --> pdb=" O VAL G 141 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N GLU G 146 " --> pdb=" O HIS G 142 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA G 147 " --> pdb=" O ARG G 143 " (cutoff:3.500A) Processing helix chain 'I' and resid 35 through 39 Processing helix chain 'I' and resid 41 through 56 removed outlier: 3.996A pdb=" N ARG I 45 " --> pdb=" O ARG I 41 " (cutoff:3.500A) Proline residue: I 51 - end of helix Processing helix chain 'I' and resid 71 through 92 Processing helix chain 'I' and resid 94 through 102 Processing helix chain 'J' and resid 14 through 32 removed outlier: 3.509A pdb=" N THR J 32 " --> pdb=" O THR J 28 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 89 removed outlier: 4.240A pdb=" N ALA J 86 " --> pdb=" O LYS J 82 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU J 87 " --> pdb=" O THR J 83 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 21 removed outlier: 3.582A pdb=" N SER M 21 " --> pdb=" O ILE M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 38 Processing helix chain 'M' and resid 49 through 63 removed outlier: 3.624A pdb=" N ILE M 53 " --> pdb=" O SER M 49 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N THR M 55 " --> pdb=" O GLY M 51 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N PHE M 63 " --> pdb=" O GLU M 59 " (cutoff:3.500A) Processing helix chain 'M' and resid 65 through 83 removed outlier: 4.405A pdb=" N LEU M 80 " --> pdb=" O SER M 76 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 93 Processing helix chain 'M' and resid 106 through 111 Processing helix chain 'N' and resid 3 through 19 Processing helix chain 'N' and resid 20 through 33 Processing helix chain 'N' and resid 39 through 49 Processing helix chain 'N' and resid 50 through 51 No H-bonds generated for 'chain 'N' and resid 50 through 51' Processing helix chain 'N' and resid 52 through 56 Processing helix chain 'N' and resid 80 through 91 removed outlier: 3.898A pdb=" N ARG N 85 " --> pdb=" O ARG N 81 " (cutoff:3.500A) Processing helix chain 'S' and resid 12 through 26 Processing sheet with id=AA1, first strand: chain 'B' and resid 31 through 35 removed outlier: 3.567A pdb=" N GLY B 33 " --> pdb=" O ILE B 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 90 through 92 removed outlier: 5.721A pdb=" N ILE B 67 " --> pdb=" O PHE B 90 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N VAL B 92 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N PHE B 69 " --> pdb=" O VAL B 92 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA B 185 " --> pdb=" O PHE B 198 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 54 through 58 Processing sheet with id=AA4, first strand: chain 'C' and resid 165 through 171 removed outlier: 5.738A pdb=" N ASP C 181 " --> pdb=" O LYS C 204 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 74 through 75 Processing sheet with id=AA6, first strand: chain 'I' and resid 6 through 11 removed outlier: 6.419A pdb=" N VAL I 29 " --> pdb=" O ILE I 65 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N VAL I 67 " --> pdb=" O VAL I 29 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 45 through 52 Processing sheet with id=AA8, first strand: chain 'J' and resid 45 through 52 removed outlier: 3.817A pdb=" N LYS N 97 " --> pdb=" O GLU J 66 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 31 through 33 removed outlier: 6.318A pdb=" N LEU S 31 " --> pdb=" O ALA S 50 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N HIS S 52 " --> pdb=" O LEU S 31 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N THR S 33 " --> pdb=" O HIS S 52 " (cutoff:3.500A) 450 hydrogen bonds defined for protein. 1290 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 256 hydrogen bonds 286 hydrogen bond angles 0 basepair planarities 116 basepair parallelities 211 stacking parallelities Total time for adding SS restraints: 4.47 Time building geometry restraints manager: 1.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2828 1.33 - 1.45: 7327 1.45 - 1.57: 8682 1.57 - 1.69: 911 1.69 - 1.81: 53 Bond restraints: 19801 Sorted by residual: bond pdb=" C5 2MG 1 966 " pdb=" C4 2MG 1 966 " ideal model delta sigma weight residual 1.382 1.468 -0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" N9 A 11105 " pdb=" C4 A 11105 " ideal model delta sigma weight residual 1.374 1.351 0.023 6.00e-03 2.78e+04 1.41e+01 bond pdb=" C5 2MG 11207 " pdb=" C4 2MG 11207 " ideal model delta sigma weight residual 1.382 1.457 -0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" N9 A 11339 " pdb=" C4 A 11339 " ideal model delta sigma weight residual 1.374 1.352 0.022 6.00e-03 2.78e+04 1.34e+01 bond pdb=" N GLY M 26 " pdb=" CA GLY M 26 " ideal model delta sigma weight residual 1.443 1.474 -0.031 8.60e-03 1.35e+04 1.28e+01 ... (remaining 19796 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 27743 2.05 - 4.11: 1098 4.11 - 6.16: 88 6.16 - 8.21: 16 8.21 - 10.26: 4 Bond angle restraints: 28949 Sorted by residual: angle pdb=" N SER I 93 " pdb=" CA SER I 93 " pdb=" C SER I 93 " ideal model delta sigma weight residual 113.88 105.93 7.95 1.23e+00 6.61e-01 4.18e+01 angle pdb=" O3' C 11103 " pdb=" C3' C 11103 " pdb=" C2' C 11103 " ideal model delta sigma weight residual 113.70 121.69 -7.99 1.50e+00 4.44e-01 2.83e+01 angle pdb=" O3' A 11157 " pdb=" C3' A 11157 " pdb=" C2' A 11157 " ideal model delta sigma weight residual 109.50 101.96 7.54 1.50e+00 4.44e-01 2.52e+01 angle pdb=" CA SER M 46 " pdb=" C SER M 46 " pdb=" O SER M 46 " ideal model delta sigma weight residual 121.56 116.31 5.25 1.09e+00 8.42e-01 2.32e+01 angle pdb=" N GLY N 68 " pdb=" CA GLY N 68 " pdb=" C GLY N 68 " ideal model delta sigma weight residual 115.72 108.87 6.85 1.51e+00 4.39e-01 2.06e+01 ... (remaining 28944 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.78: 11184 35.78 - 71.56: 1290 71.56 - 107.34: 169 107.34 - 143.12: 4 143.12 - 178.90: 4 Dihedral angle restraints: 12651 sinusoidal: 9481 harmonic: 3170 Sorted by residual: dihedral pdb=" O4' U 11008 " pdb=" C1' U 11008 " pdb=" N1 U 11008 " pdb=" C2 U 11008 " ideal model delta sinusoidal sigma weight residual 200.00 33.90 166.10 1 1.50e+01 4.44e-03 8.41e+01 dihedral pdb=" O4' U 1 960 " pdb=" C1' U 1 960 " pdb=" N1 U 1 960 " pdb=" C2 U 1 960 " ideal model delta sinusoidal sigma weight residual -128.00 50.90 -178.90 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C 11158 " pdb=" C1' C 11158 " pdb=" N1 C 11158 " pdb=" C2 C 11158 " ideal model delta sinusoidal sigma weight residual 232.00 54.69 177.31 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 12648 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 3191 0.077 - 0.154: 328 0.154 - 0.231: 79 0.231 - 0.308: 9 0.308 - 0.385: 2 Chirality restraints: 3609 Sorted by residual: chirality pdb=" C3' C 11103 " pdb=" C4' C 11103 " pdb=" O3' C 11103 " pdb=" C2' C 11103 " both_signs ideal model delta sigma weight residual False -2.48 -2.09 -0.38 2.00e-01 2.50e+01 3.70e+00 chirality pdb=" CA PHE J 49 " pdb=" N PHE J 49 " pdb=" C PHE J 49 " pdb=" CB PHE J 49 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" C3' A 1 969 " pdb=" C4' A 1 969 " pdb=" O3' A 1 969 " pdb=" C2' A 1 969 " both_signs ideal model delta sigma weight residual False -2.48 -2.78 0.30 2.00e-01 2.50e+01 2.28e+00 ... (remaining 3606 not shown) Planarity restraints: 1995 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' 2MG 11207 " -0.048 2.00e-02 2.50e+03 9.87e-02 3.17e+02 pdb=" N9 2MG 11207 " -0.020 2.00e-02 2.50e+03 pdb=" C8 2MG 11207 " 0.052 2.00e-02 2.50e+03 pdb=" N7 2MG 11207 " 0.072 2.00e-02 2.50e+03 pdb=" C5 2MG 11207 " 0.021 2.00e-02 2.50e+03 pdb=" C6 2MG 11207 " 0.004 2.00e-02 2.50e+03 pdb=" O6 2MG 11207 " 0.051 2.00e-02 2.50e+03 pdb=" N1 2MG 11207 " -0.047 2.00e-02 2.50e+03 pdb=" C2 2MG 11207 " -0.097 2.00e-02 2.50e+03 pdb=" N2 2MG 11207 " -0.142 2.00e-02 2.50e+03 pdb=" N3 2MG 11207 " -0.084 2.00e-02 2.50e+03 pdb=" C4 2MG 11207 " -0.032 2.00e-02 2.50e+03 pdb=" CM2 2MG 11207 " 0.271 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE G 26 " 0.013 2.00e-02 2.50e+03 2.65e-02 7.02e+00 pdb=" C PHE G 26 " -0.046 2.00e-02 2.50e+03 pdb=" O PHE G 26 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL G 27 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU G 120 " 0.013 2.00e-02 2.50e+03 2.63e-02 6.90e+00 pdb=" C LEU G 120 " -0.045 2.00e-02 2.50e+03 pdb=" O LEU G 120 " 0.017 2.00e-02 2.50e+03 pdb=" N ALA G 121 " 0.016 2.00e-02 2.50e+03 ... (remaining 1992 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.20: 55 2.20 - 2.87: 7424 2.87 - 3.55: 35090 3.55 - 4.22: 60082 4.22 - 4.90: 80301 Nonbonded interactions: 182952 Sorted by model distance: nonbonded pdb=" O3' U 1 952 " pdb="MG MG 11608 " model vdw 1.519 2.170 nonbonded pdb=" OP1 A 11197 " pdb="MG MG 11610 " model vdw 1.629 2.170 nonbonded pdb=" OP1 A 1 964 " pdb="MG MG 11611 " model vdw 1.659 2.170 nonbonded pdb=" OP2 C 1 972 " pdb="MG MG 11607 " model vdw 1.697 2.170 nonbonded pdb=" OP1 C 11109 " pdb="MG MG 11604 " model vdw 1.732 2.170 ... (remaining 182947 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 22.850 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.010 Internal consistency checks: 0.000 Total: 28.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.151 19802 Z= 0.604 Angle : 0.892 10.265 28949 Z= 0.721 Chirality : 0.053 0.385 3609 Planarity : 0.005 0.099 1995 Dihedral : 23.874 178.902 10599 Min Nonbonded Distance : 1.519 Molprobity Statistics. All-atom Clashscore : 42.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 0.00 % Allowed : 9.66 % Favored : 90.34 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.88 (0.23), residues: 1092 helix: -1.23 (0.22), residues: 480 sheet: -2.30 (0.36), residues: 161 loop : -2.40 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 130 TYR 0.011 0.002 TYR N 20 PHE 0.019 0.002 PHE C 37 TRP 0.012 0.002 TRP S 34 HIS 0.007 0.002 HIS M 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00703 / 0.60 (19801) covalent geometry : angle 0.89211 / 0.72 (28949) hydrogen bonds : bond 0.27501 / 27.68 ( 698) hydrogen bonds : angle 9.72030 / 11.84 ( 1576) metal coordination : bond 0.15081 / 7.54 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 LEU cc_start: 0.8915 (tp) cc_final: 0.8538 (pp) REVERT: B 129 LEU cc_start: 0.9250 (mt) cc_final: 0.9006 (tp) REVERT: B 139 ARG cc_start: 0.8057 (mtt-85) cc_final: 0.7316 (mtt180) REVERT: B 161 LEU cc_start: 0.7981 (mt) cc_final: 0.6825 (mt) REVERT: B 181 ILE cc_start: 0.8233 (mt) cc_final: 0.7913 (tp) REVERT: C 102 ASN cc_start: 0.9455 (t0) cc_final: 0.9199 (m110) REVERT: C 129 MET cc_start: 0.8870 (mmm) cc_final: 0.8227 (tpp) REVERT: C 150 LYS cc_start: 0.8551 (tttm) cc_final: 0.8065 (tptp) REVERT: C 181 ASP cc_start: 0.9054 (t0) cc_final: 0.8373 (p0) REVERT: C 203 PHE cc_start: 0.9076 (t80) cc_final: 0.8691 (t80) REVERT: G 91 VAL cc_start: 0.7421 (p) cc_final: 0.7212 (p) REVERT: I 32 GLN cc_start: 0.8757 (mm110) cc_final: 0.8547 (mm-40) REVERT: I 57 MET cc_start: 0.9379 (ptm) cc_final: 0.9035 (mmm) REVERT: I 110 GLN cc_start: 0.9585 (pt0) cc_final: 0.8757 (pm20) REVERT: I 112 GLU cc_start: 0.8217 (tt0) cc_final: 0.7750 (mp0) REVERT: J 19 ASP cc_start: 0.9199 (m-30) cc_final: 0.8907 (m-30) REVERT: J 53 ILE cc_start: 0.9180 (pt) cc_final: 0.8948 (tt) REVERT: J 63 ASP cc_start: 0.8579 (t0) cc_final: 0.7666 (t0) REVERT: J 65 TYR cc_start: 0.8477 (m-80) cc_final: 0.8111 (m-80) REVERT: M 27 LYS cc_start: 0.9409 (tppt) cc_final: 0.8780 (tppt) REVERT: M 31 LYS cc_start: 0.9248 (pttm) cc_final: 0.8922 (pttp) REVERT: M 50 GLU cc_start: 0.9519 (pm20) cc_final: 0.9141 (tm-30) REVERT: M 68 ASP cc_start: 0.9530 (m-30) cc_final: 0.9003 (t0) REVERT: M 95 LEU cc_start: 0.8930 (mt) cc_final: 0.8360 (mt) REVERT: N 86 GLU cc_start: 0.8964 (mt-10) cc_final: 0.8748 (mt-10) REVERT: N 101 TRP cc_start: 0.8402 (p90) cc_final: 0.6017 (p90) outliers start: 0 outliers final: 0 residues processed: 241 average time/residue: 0.1717 time to fit residues: 60.0840 Evaluate side-chains 145 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.2980 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 10.0000 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 HIS B 227 GLN G 122 ASN J 70 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.031563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2437 r_free = 0.2437 target = 0.022793 restraints weight = 253182.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2472 r_free = 0.2472 target = 0.023580 restraints weight = 137801.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2487 r_free = 0.2487 target = 0.023954 restraints weight = 95382.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2491 r_free = 0.2491 target = 0.024240 restraints weight = 77435.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2497 r_free = 0.2497 target = 0.024385 restraints weight = 67662.339| |-----------------------------------------------------------------------------| r_work (final): 0.2482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 19802 Z= 0.232 Angle : 0.682 12.969 28949 Z= 0.389 Chirality : 0.043 0.222 3609 Planarity : 0.007 0.086 1995 Dihedral : 25.006 178.208 8374 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 29.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.23), residues: 1092 helix: -0.72 (0.21), residues: 493 sheet: -1.93 (0.36), residues: 156 loop : -1.94 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 59 TYR 0.016 0.002 TYR I 6 PHE 0.030 0.003 PHE G 151 TRP 0.024 0.003 TRP B 96 HIS 0.006 0.002 HIS B 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.23 (19801) covalent geometry : angle 0.68225 / 0.39 (28949) hydrogen bonds : bond 0.15232 / 14.88 ( 698) hydrogen bonds : angle 6.04166 / 7.79 ( 1576) metal coordination : bond 0.00531 / 0.27 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 PHE cc_start: 0.8847 (m-10) cc_final: 0.8606 (m-80) REVERT: B 94 HIS cc_start: 0.9022 (t70) cc_final: 0.8736 (t70) REVERT: B 117 LEU cc_start: 0.8517 (mt) cc_final: 0.7816 (mt) REVERT: C 102 ASN cc_start: 0.9610 (t0) cc_final: 0.9163 (m110) REVERT: C 129 MET cc_start: 0.8844 (mmm) cc_final: 0.8265 (tpp) REVERT: C 142 MET cc_start: 0.9085 (tpp) cc_final: 0.8739 (tpt) REVERT: C 168 TYR cc_start: 0.8150 (t80) cc_final: 0.7722 (t80) REVERT: C 181 ASP cc_start: 0.8886 (t0) cc_final: 0.8162 (p0) REVERT: C 203 PHE cc_start: 0.9028 (t80) cc_final: 0.8621 (t80) REVERT: I 110 GLN cc_start: 0.9464 (pt0) cc_final: 0.8695 (pm20) REVERT: I 112 GLU cc_start: 0.8201 (tt0) cc_final: 0.7488 (mp0) REVERT: I 118 LEU cc_start: 0.9508 (mm) cc_final: 0.9263 (mt) REVERT: J 19 ASP cc_start: 0.9191 (m-30) cc_final: 0.8883 (m-30) REVERT: J 63 ASP cc_start: 0.7942 (t0) cc_final: 0.7669 (t0) REVERT: M 12 HIS cc_start: 0.8867 (p90) cc_final: 0.8490 (p-80) REVERT: M 27 LYS cc_start: 0.9333 (tppt) cc_final: 0.8761 (tppt) REVERT: M 31 LYS cc_start: 0.9267 (pttm) cc_final: 0.9063 (pttp) REVERT: M 50 GLU cc_start: 0.9528 (pm20) cc_final: 0.9142 (tm-30) REVERT: M 81 MET cc_start: 0.9103 (mtt) cc_final: 0.8834 (mtt) REVERT: N 86 GLU cc_start: 0.9412 (mt-10) cc_final: 0.9159 (mt-10) REVERT: N 89 MET cc_start: 0.9000 (mmt) cc_final: 0.8372 (mmp) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.1610 time to fit residues: 47.3798 Evaluate side-chains 131 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 102 optimal weight: 20.0000 chunk 78 optimal weight: 7.9990 chunk 46 optimal weight: 30.0000 chunk 27 optimal weight: 20.0000 chunk 87 optimal weight: 3.9990 chunk 119 optimal weight: 7.9990 chunk 48 optimal weight: 9.9990 chunk 33 optimal weight: 20.0000 chunk 118 optimal weight: 9.9990 chunk 120 optimal weight: 0.9990 chunk 136 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 GLN B 168 HIS C 140 ASN G 122 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.030650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2395 r_free = 0.2395 target = 0.022301 restraints weight = 256548.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2433 r_free = 0.2433 target = 0.022991 restraints weight = 141892.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2447 r_free = 0.2447 target = 0.023420 restraints weight = 100315.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.2453 r_free = 0.2453 target = 0.023690 restraints weight = 81207.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.2458 r_free = 0.2458 target = 0.023797 restraints weight = 71319.721| |-----------------------------------------------------------------------------| r_work (final): 0.2441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 19802 Z= 0.253 Angle : 0.646 10.906 28949 Z= 0.369 Chirality : 0.042 0.238 3609 Planarity : 0.006 0.065 1995 Dihedral : 24.936 179.559 8374 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 32.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 0.11 % Allowed : 7.27 % Favored : 92.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.24), residues: 1092 helix: -0.51 (0.22), residues: 488 sheet: -1.74 (0.36), residues: 156 loop : -1.86 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG J 68 TYR 0.018 0.002 TYR J 65 PHE 0.018 0.002 PHE C 29 TRP 0.010 0.002 TRP S 34 HIS 0.006 0.002 HIS M 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.25 (19801) covalent geometry : angle 0.64635 / 0.37 (28949) hydrogen bonds : bond 0.13653 / 13.34 ( 698) hydrogen bonds : angle 5.89242 / 7.52 ( 1576) metal coordination : bond 0.00577 / 0.29 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 175 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 94 HIS cc_start: 0.8987 (t70) cc_final: 0.8642 (t70) REVERT: B 113 ARG cc_start: 0.8710 (mtm180) cc_final: 0.8455 (mtm180) REVERT: B 186 ILE cc_start: 0.4440 (tp) cc_final: 0.4168 (tp) REVERT: C 102 ASN cc_start: 0.9606 (t0) cc_final: 0.9155 (m110) REVERT: C 129 MET cc_start: 0.8827 (mmm) cc_final: 0.8219 (tpp) REVERT: C 142 MET cc_start: 0.9164 (tpp) cc_final: 0.8919 (tpt) REVERT: C 150 LYS cc_start: 0.8577 (tttm) cc_final: 0.8098 (tptp) REVERT: C 181 ASP cc_start: 0.8957 (t0) cc_final: 0.8283 (p0) REVERT: G 15 ASP cc_start: 0.7834 (t0) cc_final: 0.7630 (t0) REVERT: G 78 ARG cc_start: 0.7701 (mpp-170) cc_final: 0.7174 (mmp-170) REVERT: I 110 GLN cc_start: 0.9504 (pt0) cc_final: 0.8614 (pm20) REVERT: I 112 GLU cc_start: 0.8318 (tt0) cc_final: 0.7564 (mp0) REVERT: J 19 ASP cc_start: 0.9226 (m-30) cc_final: 0.8932 (m-30) REVERT: J 63 ASP cc_start: 0.8498 (t0) cc_final: 0.7462 (t0) REVERT: J 88 MET cc_start: 0.9338 (mtm) cc_final: 0.9129 (mtp) REVERT: M 27 LYS cc_start: 0.9380 (tppt) cc_final: 0.8727 (tppt) REVERT: M 31 LYS cc_start: 0.9197 (pttm) cc_final: 0.8903 (pttm) REVERT: M 50 GLU cc_start: 0.9515 (pm20) cc_final: 0.9123 (tm-30) REVERT: M 72 GLU cc_start: 0.9518 (tp30) cc_final: 0.9238 (tp30) REVERT: M 81 MET cc_start: 0.9155 (mtt) cc_final: 0.8897 (mtt) REVERT: N 20 TYR cc_start: 0.9055 (m-10) cc_final: 0.8849 (m-10) REVERT: N 47 LYS cc_start: 0.9619 (tmtt) cc_final: 0.9242 (mttt) REVERT: N 86 GLU cc_start: 0.9532 (mt-10) cc_final: 0.9263 (mt-10) REVERT: S 66 MET cc_start: 0.9435 (mtp) cc_final: 0.9167 (mtp) outliers start: 1 outliers final: 1 residues processed: 176 average time/residue: 0.1610 time to fit residues: 42.2301 Evaluate side-chains 127 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 126 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 136 optimal weight: 5.9990 chunk 43 optimal weight: 20.0000 chunk 139 optimal weight: 20.0000 chunk 40 optimal weight: 20.0000 chunk 126 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 36 optimal weight: 20.0000 chunk 13 optimal weight: 30.0000 chunk 58 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 GLN B 168 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.030932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2408 r_free = 0.2408 target = 0.022405 restraints weight = 251489.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.2442 r_free = 0.2442 target = 0.023130 restraints weight = 136330.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2461 r_free = 0.2461 target = 0.023507 restraints weight = 94140.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.2468 r_free = 0.2468 target = 0.023828 restraints weight = 77297.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2473 r_free = 0.2473 target = 0.023955 restraints weight = 67598.876| |-----------------------------------------------------------------------------| r_work (final): 0.2456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 19802 Z= 0.201 Angle : 0.591 8.412 28949 Z= 0.341 Chirality : 0.040 0.237 3609 Planarity : 0.006 0.088 1995 Dihedral : 24.845 179.085 8374 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 29.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 0.11 % Allowed : 4.67 % Favored : 95.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.24), residues: 1092 helix: -0.39 (0.22), residues: 494 sheet: -1.44 (0.37), residues: 156 loop : -1.82 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 108 TYR 0.019 0.002 TYR I 6 PHE 0.023 0.002 PHE B 184 TRP 0.012 0.002 TRP G 103 HIS 0.012 0.002 HIS S 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.20 (19801) covalent geometry : angle 0.59121 / 0.34 (28949) hydrogen bonds : bond 0.12725 / 12.42 ( 698) hydrogen bonds : angle 5.67023 / 7.25 ( 1576) metal coordination : bond 0.00478 / 0.24 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 179 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 94 HIS cc_start: 0.8908 (t70) cc_final: 0.8511 (t70) REVERT: C 102 ASN cc_start: 0.9631 (t0) cc_final: 0.9183 (m110) REVERT: C 129 MET cc_start: 0.8846 (mmm) cc_final: 0.8253 (tpp) REVERT: C 142 MET cc_start: 0.9139 (tpp) cc_final: 0.8830 (tpt) REVERT: C 150 LYS cc_start: 0.8518 (tttm) cc_final: 0.8064 (tptp) REVERT: C 168 TYR cc_start: 0.8125 (t80) cc_final: 0.7418 (t80) REVERT: C 181 ASP cc_start: 0.8918 (t0) cc_final: 0.8262 (p0) REVERT: C 203 PHE cc_start: 0.8862 (t80) cc_final: 0.8423 (t80) REVERT: G 15 ASP cc_start: 0.7736 (t0) cc_final: 0.7521 (t0) REVERT: I 110 GLN cc_start: 0.9455 (pt0) cc_final: 0.8895 (pm20) REVERT: J 19 ASP cc_start: 0.9243 (m-30) cc_final: 0.8972 (m-30) REVERT: J 63 ASP cc_start: 0.8497 (t0) cc_final: 0.7703 (t0) REVERT: J 65 TYR cc_start: 0.8833 (m-80) cc_final: 0.8469 (m-80) REVERT: J 88 MET cc_start: 0.9351 (mtm) cc_final: 0.9106 (mtp) REVERT: M 12 HIS cc_start: 0.8875 (p90) cc_final: 0.8482 (p-80) REVERT: M 27 LYS cc_start: 0.9351 (tppt) cc_final: 0.8839 (tppt) REVERT: M 31 LYS cc_start: 0.9247 (pttm) cc_final: 0.9019 (pttp) REVERT: M 50 GLU cc_start: 0.9544 (pm20) cc_final: 0.9151 (tm-30) REVERT: M 68 ASP cc_start: 0.9170 (t0) cc_final: 0.8347 (t0) REVERT: M 81 MET cc_start: 0.9168 (mtt) cc_final: 0.8907 (mtt) REVERT: N 20 TYR cc_start: 0.9102 (m-10) cc_final: 0.8867 (m-10) REVERT: N 62 ASN cc_start: 0.8120 (m110) cc_final: 0.7633 (p0) REVERT: N 86 GLU cc_start: 0.9564 (mt-10) cc_final: 0.9284 (mt-10) REVERT: S 66 MET cc_start: 0.9414 (mtp) cc_final: 0.9170 (mtp) outliers start: 1 outliers final: 1 residues processed: 180 average time/residue: 0.1485 time to fit residues: 39.8347 Evaluate side-chains 130 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 129 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 131 optimal weight: 2.9990 chunk 91 optimal weight: 30.0000 chunk 82 optimal weight: 10.0000 chunk 16 optimal weight: 20.0000 chunk 32 optimal weight: 30.0000 chunk 101 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 130 optimal weight: 10.0000 chunk 108 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 89 GLN ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 GLN ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.031673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2420 r_free = 0.2420 target = 0.023269 restraints weight = 248366.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2463 r_free = 0.2463 target = 0.023963 restraints weight = 134733.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2486 r_free = 0.2486 target = 0.024466 restraints weight = 93738.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2489 r_free = 0.2489 target = 0.024695 restraints weight = 76091.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2494 r_free = 0.2494 target = 0.024822 restraints weight = 67392.157| |-----------------------------------------------------------------------------| r_work (final): 0.2473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19802 Z= 0.177 Angle : 0.578 9.424 28949 Z= 0.331 Chirality : 0.039 0.236 3609 Planarity : 0.006 0.066 1995 Dihedral : 24.772 178.976 8374 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 28.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 0.11 % Allowed : 3.69 % Favored : 96.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.24), residues: 1092 helix: -0.39 (0.22), residues: 498 sheet: -1.12 (0.37), residues: 158 loop : -1.72 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 108 TYR 0.015 0.002 TYR I 6 PHE 0.025 0.002 PHE B 126 TRP 0.010 0.002 TRP C 201 HIS 0.007 0.001 HIS S 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.18 (19801) covalent geometry : angle 0.57825 / 0.33 (28949) hydrogen bonds : bond 0.12127 / 11.83 ( 698) hydrogen bonds : angle 5.54950 / 7.06 ( 1576) metal coordination : bond 0.00447 / 0.22 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 183 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 94 HIS cc_start: 0.8810 (t70) cc_final: 0.8369 (t70) REVERT: B 109 GLN cc_start: 0.8939 (OUTLIER) cc_final: 0.8701 (pp30) REVERT: B 203 ASN cc_start: 0.6899 (t0) cc_final: 0.6430 (p0) REVERT: C 102 ASN cc_start: 0.9649 (t0) cc_final: 0.9219 (m110) REVERT: C 129 MET cc_start: 0.8810 (mmm) cc_final: 0.8215 (tpp) REVERT: C 142 MET cc_start: 0.9213 (tpp) cc_final: 0.8908 (tpt) REVERT: C 168 TYR cc_start: 0.8073 (t80) cc_final: 0.7651 (t80) REVERT: C 181 ASP cc_start: 0.8895 (t0) cc_final: 0.8299 (p0) REVERT: G 15 ASP cc_start: 0.7741 (t0) cc_final: 0.7522 (t0) REVERT: I 61 LEU cc_start: 0.9649 (mp) cc_final: 0.9416 (mt) REVERT: I 110 GLN cc_start: 0.9429 (pt0) cc_final: 0.8620 (pm20) REVERT: I 112 GLU cc_start: 0.8098 (tt0) cc_final: 0.7593 (mp0) REVERT: J 19 ASP cc_start: 0.9325 (m-30) cc_final: 0.9098 (m-30) REVERT: J 63 ASP cc_start: 0.8506 (t0) cc_final: 0.8091 (t70) REVERT: J 88 MET cc_start: 0.9331 (mtm) cc_final: 0.9056 (mtp) REVERT: M 12 HIS cc_start: 0.8895 (p90) cc_final: 0.8526 (p-80) REVERT: M 27 LYS cc_start: 0.9341 (tppt) cc_final: 0.8970 (tppt) REVERT: M 50 GLU cc_start: 0.9554 (pm20) cc_final: 0.9189 (tm-30) REVERT: M 81 MET cc_start: 0.9143 (mtt) cc_final: 0.8860 (mtt) REVERT: N 20 TYR cc_start: 0.9078 (m-10) cc_final: 0.8867 (m-10) REVERT: N 86 GLU cc_start: 0.9572 (mt-10) cc_final: 0.9315 (mt-10) REVERT: S 17 LYS cc_start: 0.9564 (mptt) cc_final: 0.9342 (mttt) REVERT: S 66 MET cc_start: 0.9368 (mtp) cc_final: 0.9162 (mtp) outliers start: 1 outliers final: 0 residues processed: 184 average time/residue: 0.1651 time to fit residues: 44.2333 Evaluate side-chains 125 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 124 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 94 optimal weight: 8.9990 chunk 36 optimal weight: 30.0000 chunk 48 optimal weight: 40.0000 chunk 105 optimal weight: 4.9990 chunk 91 optimal weight: 20.0000 chunk 64 optimal weight: 0.2980 chunk 86 optimal weight: 6.9990 chunk 148 optimal weight: 9.9990 chunk 39 optimal weight: 20.0000 chunk 71 optimal weight: 0.7980 chunk 114 optimal weight: 4.9990 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 GLN B 120 GLN B 168 HIS ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.031229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2421 r_free = 0.2421 target = 0.022623 restraints weight = 247453.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2458 r_free = 0.2458 target = 0.023323 restraints weight = 134068.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.2472 r_free = 0.2472 target = 0.023765 restraints weight = 93914.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2481 r_free = 0.2481 target = 0.023978 restraints weight = 75762.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2487 r_free = 0.2487 target = 0.024147 restraints weight = 68038.225| |-----------------------------------------------------------------------------| r_work (final): 0.2469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19802 Z= 0.181 Angle : 0.587 8.023 28949 Z= 0.335 Chirality : 0.039 0.230 3609 Planarity : 0.007 0.133 1995 Dihedral : 24.713 179.123 8374 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 27.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 0.11 % Allowed : 3.15 % Favored : 96.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.24), residues: 1092 helix: -0.22 (0.22), residues: 497 sheet: -1.09 (0.37), residues: 159 loop : -1.67 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG S 3 TYR 0.014 0.002 TYR J 65 PHE 0.018 0.002 PHE B 126 TRP 0.022 0.002 TRP N 101 HIS 0.009 0.002 HIS B 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.18 (19801) covalent geometry : angle 0.58733 / 0.34 (28949) hydrogen bonds : bond 0.11859 / 11.55 ( 698) hydrogen bonds : angle 5.48453 / 6.90 ( 1576) metal coordination : bond 0.00515 / 0.26 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 171 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 94 HIS cc_start: 0.8811 (t70) cc_final: 0.8317 (t70) REVERT: C 102 ASN cc_start: 0.9664 (t0) cc_final: 0.9237 (m110) REVERT: C 129 MET cc_start: 0.8827 (mmm) cc_final: 0.8237 (tpp) REVERT: C 142 MET cc_start: 0.9247 (tpp) cc_final: 0.8984 (tpt) REVERT: C 168 TYR cc_start: 0.8051 (t80) cc_final: 0.7656 (t80) REVERT: C 181 ASP cc_start: 0.8913 (t0) cc_final: 0.8315 (p0) REVERT: G 15 ASP cc_start: 0.7889 (t0) cc_final: 0.7622 (t0) REVERT: I 61 LEU cc_start: 0.9634 (mp) cc_final: 0.9327 (mt) REVERT: I 110 GLN cc_start: 0.9450 (pt0) cc_final: 0.8648 (pm20) REVERT: I 111 VAL cc_start: 0.9357 (p) cc_final: 0.8785 (p) REVERT: I 112 GLU cc_start: 0.8122 (tt0) cc_final: 0.7605 (mp0) REVERT: J 19 ASP cc_start: 0.9303 (m-30) cc_final: 0.8922 (m-30) REVERT: J 63 ASP cc_start: 0.8461 (t0) cc_final: 0.8014 (t70) REVERT: M 12 HIS cc_start: 0.8921 (p90) cc_final: 0.8559 (p-80) REVERT: M 27 LYS cc_start: 0.9345 (tppt) cc_final: 0.8980 (tppt) REVERT: M 50 GLU cc_start: 0.9561 (pm20) cc_final: 0.9082 (tm-30) REVERT: M 75 MET cc_start: 0.9513 (ptp) cc_final: 0.9148 (mmt) REVERT: M 81 MET cc_start: 0.9159 (mtt) cc_final: 0.8872 (mtt) REVERT: N 20 TYR cc_start: 0.9147 (m-10) cc_final: 0.8935 (m-10) REVERT: N 86 GLU cc_start: 0.9582 (mt-10) cc_final: 0.9375 (mt-10) REVERT: S 17 LYS cc_start: 0.9595 (mptt) cc_final: 0.9359 (mttt) REVERT: S 66 MET cc_start: 0.9326 (mtp) cc_final: 0.9108 (mtp) outliers start: 1 outliers final: 1 residues processed: 172 average time/residue: 0.1449 time to fit residues: 37.2833 Evaluate side-chains 123 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 122 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 50 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 148 optimal weight: 9.9990 chunk 146 optimal weight: 0.7980 chunk 66 optimal weight: 20.0000 chunk 4 optimal weight: 30.0000 chunk 94 optimal weight: 10.0000 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 GLN ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 66 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.031819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2424 r_free = 0.2424 target = 0.023328 restraints weight = 245356.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2468 r_free = 0.2468 target = 0.024046 restraints weight = 132405.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.2482 r_free = 0.2482 target = 0.024503 restraints weight = 92130.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2493 r_free = 0.2493 target = 0.024768 restraints weight = 74235.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2497 r_free = 0.2497 target = 0.024940 restraints weight = 65635.815| |-----------------------------------------------------------------------------| r_work (final): 0.2481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 19802 Z= 0.172 Angle : 0.569 7.931 28949 Z= 0.325 Chirality : 0.038 0.266 3609 Planarity : 0.006 0.079 1995 Dihedral : 24.660 179.402 8374 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 27.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 0.11 % Allowed : 2.28 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.24), residues: 1092 helix: -0.18 (0.22), residues: 507 sheet: -0.93 (0.37), residues: 161 loop : -1.66 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG S 3 TYR 0.012 0.001 TYR I 6 PHE 0.018 0.002 PHE N 77 TRP 0.012 0.002 TRP N 101 HIS 0.006 0.001 HIS B 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.17 (19801) covalent geometry : angle 0.56943 / 0.32 (28949) hydrogen bonds : bond 0.11540 / 11.26 ( 698) hydrogen bonds : angle 5.34405 / 6.77 ( 1576) metal coordination : bond 0.00063 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 168 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 102 ASN cc_start: 0.9665 (t0) cc_final: 0.9251 (m110) REVERT: C 129 MET cc_start: 0.8818 (mmm) cc_final: 0.8229 (tpp) REVERT: C 142 MET cc_start: 0.9221 (tpp) cc_final: 0.9009 (tpt) REVERT: C 168 TYR cc_start: 0.8057 (t80) cc_final: 0.7663 (t80) REVERT: C 181 ASP cc_start: 0.8888 (t0) cc_final: 0.8297 (p0) REVERT: G 15 ASP cc_start: 0.7716 (t0) cc_final: 0.7421 (t0) REVERT: I 61 LEU cc_start: 0.9650 (mp) cc_final: 0.9371 (mt) REVERT: I 112 GLU cc_start: 0.8213 (tt0) cc_final: 0.7731 (mp0) REVERT: J 19 ASP cc_start: 0.9238 (m-30) cc_final: 0.8937 (m-30) REVERT: J 63 ASP cc_start: 0.8586 (t0) cc_final: 0.7845 (t70) REVERT: J 65 TYR cc_start: 0.9116 (m-80) cc_final: 0.8387 (m-80) REVERT: M 12 HIS cc_start: 0.8860 (p90) cc_final: 0.8497 (p-80) REVERT: M 27 LYS cc_start: 0.9360 (tppt) cc_final: 0.8996 (tppt) REVERT: M 50 GLU cc_start: 0.9544 (pm20) cc_final: 0.9077 (tm-30) REVERT: M 68 ASP cc_start: 0.9206 (t0) cc_final: 0.8489 (t0) REVERT: M 81 MET cc_start: 0.9138 (mtt) cc_final: 0.8834 (mtt) REVERT: N 20 TYR cc_start: 0.9148 (m-10) cc_final: 0.8921 (m-10) REVERT: N 47 LYS cc_start: 0.9625 (tmtt) cc_final: 0.9266 (mttt) REVERT: N 82 ILE cc_start: 0.9134 (mt) cc_final: 0.8568 (mt) REVERT: N 86 GLU cc_start: 0.9572 (mt-10) cc_final: 0.9356 (mp0) REVERT: S 17 LYS cc_start: 0.9614 (mptt) cc_final: 0.9390 (mttt) outliers start: 1 outliers final: 1 residues processed: 169 average time/residue: 0.1435 time to fit residues: 37.1968 Evaluate side-chains 122 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 121 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 89 optimal weight: 30.0000 chunk 61 optimal weight: 8.9990 chunk 84 optimal weight: 1.9990 chunk 26 optimal weight: 20.0000 chunk 76 optimal weight: 0.9990 chunk 79 optimal weight: 7.9990 chunk 69 optimal weight: 0.4980 chunk 10 optimal weight: 20.0000 chunk 63 optimal weight: 10.0000 chunk 143 optimal weight: 1.9990 chunk 125 optimal weight: 0.6980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 GLN ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.032270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2458 r_free = 0.2458 target = 0.023405 restraints weight = 241673.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2499 r_free = 0.2499 target = 0.024160 restraints weight = 129736.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.2512 r_free = 0.2512 target = 0.024627 restraints weight = 89376.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2523 r_free = 0.2523 target = 0.024919 restraints weight = 71712.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2528 r_free = 0.2528 target = 0.025030 restraints weight = 63395.498| |-----------------------------------------------------------------------------| r_work (final): 0.2510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 19802 Z= 0.132 Angle : 0.564 7.587 28949 Z= 0.318 Chirality : 0.037 0.237 3609 Planarity : 0.006 0.069 1995 Dihedral : 24.512 179.609 8374 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 23.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.11 % Allowed : 1.95 % Favored : 97.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.24), residues: 1092 helix: -0.21 (0.22), residues: 508 sheet: -0.84 (0.36), residues: 167 loop : -1.40 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG N 9 TYR 0.009 0.001 TYR B 213 PHE 0.025 0.002 PHE B 91 TRP 0.022 0.002 TRP N 101 HIS 0.004 0.001 HIS J 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.13 (19801) covalent geometry : angle 0.56380 / 0.32 (28949) hydrogen bonds : bond 0.11247 / 10.97 ( 698) hydrogen bonds : angle 5.21560 / 6.59 ( 1576) metal coordination : bond 0.00209 / 0.10 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 176 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 94 HIS cc_start: 0.8677 (t70) cc_final: 0.8108 (t70) REVERT: B 109 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.8727 (pp30) REVERT: C 102 ASN cc_start: 0.9659 (t0) cc_final: 0.9269 (m110) REVERT: C 129 MET cc_start: 0.8739 (mmm) cc_final: 0.8131 (tpp) REVERT: C 142 MET cc_start: 0.9202 (tpp) cc_final: 0.8957 (tpt) REVERT: C 168 TYR cc_start: 0.8112 (t80) cc_final: 0.7656 (t80) REVERT: C 181 ASP cc_start: 0.8892 (t0) cc_final: 0.8338 (p0) REVERT: G 15 ASP cc_start: 0.7622 (t0) cc_final: 0.7411 (t0) REVERT: G 31 MET cc_start: 0.6132 (ptt) cc_final: 0.5921 (ptt) REVERT: G 38 THR cc_start: 0.8971 (p) cc_final: 0.8738 (t) REVERT: G 78 ARG cc_start: 0.7551 (mpp-170) cc_final: 0.7110 (mmm160) REVERT: I 61 LEU cc_start: 0.9554 (mp) cc_final: 0.9245 (mt) REVERT: I 110 GLN cc_start: 0.9451 (pt0) cc_final: 0.8948 (pm20) REVERT: J 11 LYS cc_start: 0.8547 (mptt) cc_final: 0.8196 (mmmt) REVERT: J 19 ASP cc_start: 0.9281 (m-30) cc_final: 0.9008 (m-30) REVERT: J 63 ASP cc_start: 0.8535 (t0) cc_final: 0.7758 (t70) REVERT: J 65 TYR cc_start: 0.9117 (m-80) cc_final: 0.8380 (m-80) REVERT: J 66 GLU cc_start: 0.6248 (tm-30) cc_final: 0.5470 (tm-30) REVERT: M 12 HIS cc_start: 0.8912 (p90) cc_final: 0.8578 (p-80) REVERT: M 27 LYS cc_start: 0.9357 (tppt) cc_final: 0.8845 (tppt) REVERT: M 50 GLU cc_start: 0.9567 (pm20) cc_final: 0.9094 (tm-30) REVERT: M 81 MET cc_start: 0.9110 (mtt) cc_final: 0.8808 (mtt) REVERT: N 20 TYR cc_start: 0.9120 (m-10) cc_final: 0.8879 (m-10) REVERT: N 47 LYS cc_start: 0.9632 (tmtt) cc_final: 0.9312 (mttt) REVERT: S 66 MET cc_start: 0.9187 (mtp) cc_final: 0.8898 (mtp) outliers start: 1 outliers final: 0 residues processed: 177 average time/residue: 0.1478 time to fit residues: 38.6090 Evaluate side-chains 125 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 124 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 35 optimal weight: 30.0000 chunk 5 optimal weight: 20.0000 chunk 139 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 46 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 143 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 13 optimal weight: 30.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 GLN ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 ASN ** J 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.031095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2409 r_free = 0.2409 target = 0.022484 restraints weight = 250959.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2451 r_free = 0.2451 target = 0.023186 restraints weight = 138529.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2466 r_free = 0.2466 target = 0.023599 restraints weight = 97559.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2474 r_free = 0.2474 target = 0.023797 restraints weight = 78987.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.2475 r_free = 0.2475 target = 0.023981 restraints weight = 71224.566| |-----------------------------------------------------------------------------| r_work (final): 0.2460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 19802 Z= 0.215 Angle : 0.622 11.725 28949 Z= 0.351 Chirality : 0.040 0.310 3609 Planarity : 0.006 0.122 1995 Dihedral : 24.568 179.811 8374 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 31.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.11 % Allowed : 0.33 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.24), residues: 1092 helix: -0.35 (0.22), residues: 511 sheet: -1.22 (0.36), residues: 172 loop : -1.49 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG G 10 TYR 0.012 0.002 TYR J 65 PHE 0.018 0.002 PHE B 91 TRP 0.012 0.002 TRP N 101 HIS 0.009 0.002 HIS J 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.22 (19801) covalent geometry : angle 0.62235 / 0.35 (28949) hydrogen bonds : bond 0.11481 / 11.26 ( 698) hydrogen bonds : angle 5.52955 / 6.94 ( 1576) metal coordination : bond 0.00610 / 0.31 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 158 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 94 HIS cc_start: 0.8710 (t70) cc_final: 0.8184 (t70) REVERT: B 109 GLN cc_start: 0.8981 (OUTLIER) cc_final: 0.8744 (pp30) REVERT: C 102 ASN cc_start: 0.9611 (t0) cc_final: 0.9272 (m110) REVERT: C 129 MET cc_start: 0.8819 (mmm) cc_final: 0.8236 (tpp) REVERT: C 142 MET cc_start: 0.9264 (tpp) cc_final: 0.8990 (tpt) REVERT: C 168 TYR cc_start: 0.8116 (t80) cc_final: 0.7754 (t80) REVERT: C 181 ASP cc_start: 0.8921 (t0) cc_final: 0.8356 (p0) REVERT: G 15 ASP cc_start: 0.7770 (t0) cc_final: 0.7471 (t0) REVERT: G 78 ARG cc_start: 0.7605 (mpp-170) cc_final: 0.7065 (mmm160) REVERT: I 42 GLU cc_start: 0.9410 (tm-30) cc_final: 0.9091 (tp30) REVERT: I 61 LEU cc_start: 0.9580 (mp) cc_final: 0.9275 (mt) REVERT: J 19 ASP cc_start: 0.9282 (m-30) cc_final: 0.8986 (m-30) REVERT: J 63 ASP cc_start: 0.8564 (t0) cc_final: 0.7831 (t70) REVERT: J 65 TYR cc_start: 0.9083 (m-80) cc_final: 0.8339 (m-80) REVERT: M 12 HIS cc_start: 0.8869 (p90) cc_final: 0.8622 (p-80) REVERT: M 27 LYS cc_start: 0.9320 (tppt) cc_final: 0.8916 (tppt) REVERT: M 50 GLU cc_start: 0.9557 (pm20) cc_final: 0.9229 (tm-30) REVERT: M 81 MET cc_start: 0.9155 (mtt) cc_final: 0.8890 (mtt) REVERT: N 20 TYR cc_start: 0.9143 (m-10) cc_final: 0.8914 (m-10) REVERT: S 66 MET cc_start: 0.9218 (mtp) cc_final: 0.8987 (mtp) outliers start: 1 outliers final: 0 residues processed: 159 average time/residue: 0.1323 time to fit residues: 32.0982 Evaluate side-chains 119 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 118 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 152 optimal weight: 5.9990 chunk 146 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 chunk 109 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 chunk 133 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 chunk 36 optimal weight: 30.0000 chunk 9 optimal weight: 30.0000 chunk 62 optimal weight: 0.9980 chunk 85 optimal weight: 7.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 GLN ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.031648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2430 r_free = 0.2430 target = 0.022881 restraints weight = 246074.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2471 r_free = 0.2471 target = 0.023628 restraints weight = 134236.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2487 r_free = 0.2487 target = 0.024054 restraints weight = 92885.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.2493 r_free = 0.2493 target = 0.024318 restraints weight = 74863.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2499 r_free = 0.2499 target = 0.024455 restraints weight = 65972.698| |-----------------------------------------------------------------------------| r_work (final): 0.2486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.4294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 19802 Z= 0.165 Angle : 0.586 11.796 28949 Z= 0.331 Chirality : 0.039 0.332 3609 Planarity : 0.006 0.096 1995 Dihedral : 24.557 179.064 8374 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 26.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 0.11 % Allowed : 0.43 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.25), residues: 1092 helix: -0.31 (0.22), residues: 505 sheet: -0.97 (0.37), residues: 167 loop : -1.38 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G 10 TYR 0.011 0.001 TYR G 44 PHE 0.034 0.002 PHE B 50 TRP 0.014 0.002 TRP N 101 HIS 0.005 0.001 HIS S 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.17 (19801) covalent geometry : angle 0.58621 / 0.33 (28949) hydrogen bonds : bond 0.11294 / 11.07 ( 698) hydrogen bonds : angle 5.42269 / 6.73 ( 1576) metal coordination : bond 0.00438 / 0.22 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 154 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 PHE cc_start: 0.9151 (m-80) cc_final: 0.8895 (m-10) REVERT: B 94 HIS cc_start: 0.8642 (t70) cc_final: 0.8091 (t70) REVERT: B 109 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.8739 (pp30) REVERT: C 102 ASN cc_start: 0.9618 (t0) cc_final: 0.9271 (m110) REVERT: C 129 MET cc_start: 0.8763 (mmm) cc_final: 0.8204 (tpp) REVERT: C 142 MET cc_start: 0.9224 (tpp) cc_final: 0.8956 (tpt) REVERT: C 168 TYR cc_start: 0.8152 (t80) cc_final: 0.7708 (t80) REVERT: C 181 ASP cc_start: 0.8886 (t0) cc_final: 0.8303 (p0) REVERT: G 15 ASP cc_start: 0.7652 (t0) cc_final: 0.7366 (t0) REVERT: G 78 ARG cc_start: 0.7539 (mpp-170) cc_final: 0.7053 (mmm160) REVERT: I 42 GLU cc_start: 0.9457 (tm-30) cc_final: 0.9080 (tp30) REVERT: I 61 LEU cc_start: 0.9621 (mp) cc_final: 0.9279 (mt) REVERT: I 118 LEU cc_start: 0.9392 (mm) cc_final: 0.9158 (mt) REVERT: J 63 ASP cc_start: 0.8592 (t0) cc_final: 0.7890 (t70) REVERT: J 65 TYR cc_start: 0.9125 (m-80) cc_final: 0.8463 (m-80) REVERT: J 88 MET cc_start: 0.9518 (mpp) cc_final: 0.9234 (mpp) REVERT: M 12 HIS cc_start: 0.8902 (p90) cc_final: 0.8556 (p-80) REVERT: M 27 LYS cc_start: 0.9285 (tppt) cc_final: 0.8893 (tppt) REVERT: M 50 GLU cc_start: 0.9572 (pm20) cc_final: 0.9040 (tp30) REVERT: M 81 MET cc_start: 0.9112 (mtt) cc_final: 0.8874 (mtt) REVERT: N 20 TYR cc_start: 0.9134 (m-10) cc_final: 0.8895 (m-10) REVERT: S 66 MET cc_start: 0.9224 (mtp) cc_final: 0.8976 (mtp) outliers start: 1 outliers final: 0 residues processed: 155 average time/residue: 0.1284 time to fit residues: 30.9510 Evaluate side-chains 128 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 127 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 110 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 86 optimal weight: 5.9990 chunk 46 optimal weight: 20.0000 chunk 19 optimal weight: 20.0000 chunk 121 optimal weight: 7.9990 chunk 83 optimal weight: 6.9990 chunk 30 optimal weight: 30.0000 chunk 75 optimal weight: 0.9980 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 GLN ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.031809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2426 r_free = 0.2426 target = 0.023316 restraints weight = 245975.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2467 r_free = 0.2467 target = 0.024037 restraints weight = 135616.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2482 r_free = 0.2482 target = 0.024475 restraints weight = 94955.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.2488 r_free = 0.2488 target = 0.024718 restraints weight = 76514.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2494 r_free = 0.2494 target = 0.024849 restraints weight = 67312.783| |-----------------------------------------------------------------------------| r_work (final): 0.2479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19802 Z= 0.182 Angle : 0.588 7.759 28949 Z= 0.334 Chirality : 0.039 0.286 3609 Planarity : 0.006 0.083 1995 Dihedral : 24.539 179.498 8374 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 27.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 0.11 % Allowed : 0.65 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.25), residues: 1092 helix: -0.29 (0.22), residues: 504 sheet: -1.09 (0.38), residues: 170 loop : -1.31 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 108 TYR 0.010 0.002 TYR J 65 PHE 0.019 0.002 PHE B 91 TRP 0.012 0.002 TRP B 104 HIS 0.005 0.001 HIS B 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.18 (19801) covalent geometry : angle 0.58806 / 0.33 (28949) hydrogen bonds : bond 0.11184 / 10.97 ( 698) hydrogen bonds : angle 5.43892 / 6.74 ( 1576) metal coordination : bond 0.00502 / 0.25 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2670.87 seconds wall clock time: 47 minutes 45.70 seconds (2865.70 seconds total)